# HG changeset patch
# User peterjc
# Date 1432221823 14400
# Node ID 438d756f348b0a3a8636d4f6d07c284d6a102886
# Parent  ccebb3dcda8857aeb64de6016168f39f9b705887
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4_assembler commit ec7b3da3689454591923d0ef3da9ab5a3c370ed4

diff -r ccebb3dcda88 -r 438d756f348b tools/mira4_assembler/README.rst
--- a/tools/mira4_assembler/README.rst	Thu May 21 10:50:36 2015 -0400
+++ b/tools/mira4_assembler/README.rst	Thu May 21 11:23:43 2015 -0400
@@ -102,6 +102,7 @@
         - Reorder XML elements (internal change only).
         - Use the ``format_source=...`` tag in the MIRA bait wrapper.
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+        - MIRA 4.0.2 dependency now declared via dedicated Tool Shed package.
 ======= ======================================================================
 
 
diff -r ccebb3dcda88 -r 438d756f348b tools/mira4_assembler/mira4_de_novo.xml
--- a/tools/mira4_assembler/mira4_de_novo.xml	Thu May 21 10:50:36 2015 -0400
+++ b/tools/mira4_assembler/mira4_de_novo.xml	Thu May 21 11:23:43 2015 -0400
@@ -3,7 +3,7 @@
     <requirements>
         <requirement type="binary">mira</requirement>
         <requirement type="binary">miraconvert</requirement>
-        <requirement type="package" version="4.0">MIRA</requirement>
+        <requirement type="package" version="4.0.2">MIRA</requirement>
         <requirement type="binary">samtools</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
diff -r ccebb3dcda88 -r 438d756f348b tools/mira4_assembler/mira4_mapping.xml
--- a/tools/mira4_assembler/mira4_mapping.xml	Thu May 21 10:50:36 2015 -0400
+++ b/tools/mira4_assembler/mira4_mapping.xml	Thu May 21 11:23:43 2015 -0400
@@ -3,7 +3,7 @@
     <requirements>
         <requirement type="binary">mira</requirement>
         <requirement type="binary">miraconvert</requirement>
-        <requirement type="package" version="4.0">MIRA</requirement>
+        <requirement type="package" version="4.0.2">MIRA</requirement>
         <requirement type="binary">samtools</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
diff -r ccebb3dcda88 -r 438d756f348b tools/mira4_assembler/tool_dependencies.xml
--- a/tools/mira4_assembler/tool_dependencies.xml	Thu May 21 10:50:36 2015 -0400
+++ b/tools/mira4_assembler/tool_dependencies.xml	Thu May 21 11:23:43 2015 -0400
@@ -3,53 +3,7 @@
     <package name="samtools" version="0.1.19">
         <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="MIRA" version="4.0">
-        <install version="1.0">
-            <actions_group>
-                <!-- Download the binaries for MIRA compatible with 64-bit OSX. -->
-                <actions architecture="x86_64" os="darwin">
-                    <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_darwin13.1.0_x86_64_static.tar.bz2</action>
-                    <action type="move_directory_files">
-                         <source_directory>bin</source_directory>
-                         <destination_directory>$INSTALL_DIR</destination_directory>
-                     </action>
-                </actions>
-                <!-- Download the binaries for MIRA compatible with 64-bit Linux. -->
-                <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_linux-gnu_x86_64_static.tar.bz2</action>
-                    <action type="move_directory_files">
-                        <source_directory>bin</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
-                <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
-                <actions>
-                    <action type="shell_command">echo "ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported."</action>
-                    <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action>
-                    <action type="shell_command">uname</action>
-                    <action type="shell_command">arch</action>
-                    <action type="shell_command">echo "If pre-compiled MIRA binaries are now available for this, please report this"</action>
-                    <action type="shell_command">echo "via https://github.com/peterjc/pico_galaxyt/issues - thank you!"</action>
-                    <action type="shell_command">false</action>
-                    <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install -->
-                </actions>
-                <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="set_to" name="MIRA4">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions_group>
-        </install>
-        <readme>
-Downloads MIRA v4.0.2 from Sourceforge, requesting Bastien's precompiled binaries
-for 64 bit (x86_64) Linux or Mac OS X. Other platforms where compilation from
-source would be required (e.g. 32 bit Linux) are not supported by this automated
-installation script.
-
-http://chevreux.org/projects_mira.html
-http://sourceforge.net/projects/mira-assembler/
-        </readme>
+    <package name="MIRA" version="4.0.2">
+        <repository changeset_revision="4be5c2deb512" name="package_mira_4_0_2" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>